org.jmol.jvxl.readers

Class PolygonFileReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.PolygonFileReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

EfvetReader, PmeshReader

abstract class PolygonFileReader
extends SurfaceFileReader

Field Summary

Fields

Modifier and Type	Field and Description
protected int	nTriangles
protected int	nVertices

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next, os

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes

Constructor Summary

Constructors

Constructor and Description
PolygonFileReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
(package private) abstract void	getSurfaceData()
protected void	readSurfaceData(boolean isMapData)
protected boolean	readVolumeData(boolean isMapData)
protected boolean	readVolumeParameters(boolean isMapData)

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

closeReader, discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nVertices

protected int nVertices

nTriangles

protected int nTriangles

Constructor Detail

PolygonFileReader

PolygonFileReader(SurfaceGenerator sg,
                 java.io.BufferedReader br)

Method Detail

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)

Specified by:

readVolumeParameters in class SurfaceReader

readVolumeData

protected boolean readVolumeData(boolean isMapData)

Specified by:

readVolumeData in class SurfaceReader

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception

Specified by:

readSurfaceData in class SurfaceReader

Throws:

java.lang.Exception

getSurfaceData

abstract void getSurfaceData()
                      throws java.lang.Exception

Throws:

java.lang.Exception